BN1855 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 9.5918e-08 3.2947e-05
Layer 5 6.0565e-07 3.0199e-05
Layer 3 1.4888e-06 6.3035e-03
Layer 6 9.8027e-06 1.3003e-03
Layer 2 2.2471e-05 1.2521e-02
Layer 1 9.6136e-01 7.9219e-01
WM 9.7613e-01 6.4624e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
CD200 Expression Distribution
Gene Specificity Score (GSS)
CD200 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
CD200 Layer 5 2.9092 0.8157
ELMOD1 Layer 5 2.8252 0.8003
CAMK2D Layer 5 3.1973 0.8002
NDRG3 Layer 5 2.4756 0.7990
ATXN7L3B Layer 4 2.7305 0.7969
FKBP3 Layer 5 2.7100 0.7968
SH3GL2 Layer 5 2.8965 0.7961
PNMA8A Layer 5 2.7188 0.7933
HPRT1 Layer 5 2.6191 0.7926
EPHA4 Layer 4 2.9961 0.7914
MDH2 Layer 5 2.6689 0.7912
MOAP1 Layer 5 2.8115 0.7901
GLS Layer 5 2.7910 0.7894
SLC39A10 Layer 5 2.7822 0.7892
CLSTN3 Layer 5 2.9434 0.7884
SYNGR3 Layer 5 2.7480 0.7883
GABRG2 Layer 5 2.7217 0.7880
NUDT4 Layer 5 2.9160 0.7877
DYNC1I1 Layer 5 3.1191 0.7860
SULT4A1 Layer 4 2.8057 0.7840
PPP2R2B Layer 5 2.7422 0.7822
PDXP Layer 5 2.5605 0.7818
DOCK3 Layer 5 2.6777 0.7800
BSN Layer 5 2.7070 0.7796
ATXN10 Layer 5 2.7910 0.7796
ATP6V1G1 Layer 5 2.4453 0.7791
PNMA1 Layer 5 2.5723 0.7788
CHGA Layer 5 2.6484 0.7776
SLC9A6 Layer 5 2.7070 0.7768
VDAC2 Layer 4 2.5566 0.7768
TUBB3 Layer 5 2.7686 0.7757
SUMO1 Layer 5 2.6602 0.7732
VDAC1 Layer 5 2.5566 0.7729
CMAS Layer 5 3.1221 0.7723
GABARAPL1 Layer 5 2.4453 0.7717
ATP6V1A Layer 5 2.6426 0.7717
PFKP Layer 5 3.1152 0.7716
RAB11A Layer 5 2.3867 0.7715
STRAP Layer 5 2.8398 0.7713
SYNGR1 Layer 5 2.6543 0.7713
AARS Layer 5 2.6221 0.7706
DDB1 Layer 5 2.3809 0.7706
INPP5F Layer 4 2.7188 0.7705
MAPK9 Layer 5 2.8906 0.7705
PPM1A Layer 5 2.7188 0.7697
KCNC2 Layer 5 2.5420 0.7690
ATL1 Layer 5 2.7246 0.7685
SATB1 Layer 4 3.2793 0.7683
REEP1 Layer 5 2.8369 0.7674
KIF3A Layer 5 2.7393 0.7674

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1855
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1855_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1855/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1855/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1855/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1855/report/PD/BN1855_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1855/report/PD/BN1855_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:52:19
  • Number of Processes: 10
  • Spending Time: 0h 3m